MmuINT0028676 @ mm10
Intron Retention
Gene
ENSMUSG00000058626 | Capn11
Description
calpain 11 [Source:MGI Symbol;Acc:MGI:1352490]
Coordinates
chr17:45632009-45632449:-
Coord C1 exon
chr17:45632381-45632449
Coord A exon
chr17:45632088-45632380
Coord C2 exon
chr17:45632009-45632087
Length
293 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGG
5' ss Score
10.38
3' ss Seq
ACGTCTCTGTCTGTCTTCAGGAA
3' ss Score
12.33
Exon sequences
Seq C1 exon
AAAGATGGTTCTGGCAAGCTGGAGCTTCATGAATTCCAGGTCCTGTGGAAAAAGATCAAGAAATGGACG
Seq A exon
GTAAGGGACCCTTAAAGAGCCAAGAGGCGTGGGAATGGACAAAGAAGCCATTAGAACTATACACACACACACACACACACACACACACACAGAGTCAAACTGGTTAGTAACCAGTATAGCCTGTTATAGTCATGAAGGGTTTGCTAGAAGGCAGGAACATTAGAGATCCAAGTGGCTGATCAGAGGGGGCAGGGGGAAGCCCCAGAGTCTAGGGCAGATGTCATAAGCCAGTCATGCTTGAGTATTCTGTTTTTCAACCACCGTGACCTGATGACGTCTCTGTCTGTCTTCAG
Seq C2 exon
GAAATCTTCAAAGAGTGTGATGAGGACCGCTCAGGGAACTTGAACTCCTATGAGATGCGCCTGGCAATAGAGAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058626:ENSMUST00000120717:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138331=EF-hand_8=PD(29.5=78.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGATGGTTCTGGCAAGCTGG
R:
CTGCTTTCTCTATTGCCAGGC
Band lengths:
148-441
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types